Predicting regulons and their cis-regulatory motifs by comparative genomics

We have combined and compared three techniques for predicting functional in teractions based on comparative genomics (methods based on conserved operon s, protein fusions and correlated evolution) and optimized these methods to predict coregulated seas of genes in 24 complete genomes, including Saccha romyces cerevisiae, Caenorhabditis elegans and 22 prokaryotes. The method b ased on conserved operons was the most useful for this purpose. Upstream re gions of the genes comprising these predicted regulons were then used to se arch for regulatory motifs in 22 prokaryotic genomes using the motif-discov ery program AlignACE, Many significant upstream motifs, including five know n Escherichia coli regulatory motifs, were identified in this manner. The p resence of a significant regulatory motif was used to refine the members of the predicted regulons to generate a final set of predicted regulons that share significant regulatory elements.